July 2004 Archives by thread

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Starting: Thu Jul 1 07:53:09 EST 2004
Ending: Sat Jul 31 14:05:41 EST 2004
Messages: 262

• [Bioperl-l] parsing GenScan result   Yin Yanbin
  • [Bioperl-l] parsing GenScan result   Brian Osborne
• [Bioperl-l] PDB sequence from ATOM records   Matthew Betts
• [Bioperl-l] PDB sequence from ATOM records   Matthew Betts
• [Bioperl-l] blast/cgi question   Huizhuan Wu
  • [Bioperl-l] blast/cgi question   Brian Osborne
• [Bioperl-l] Re: [Bioperl-guts-l] blast/cgi question   Jason Stajich
  • [Bioperl-l] Re: [Bioperl-guts-l] blast/cgi question   Huizhuan Wu
• [Bioperl-l] Problems parsing swiss-prot files   Jessica Dantzer
  • [Bioperl-l] Problems parsing swiss-prot files   Jason Stajich
• [Bioperl-l] search2gff   Neil Saunders
  • [Bioperl-l] search2gff   Jason Stajich
• [Bioperl-l] RE: blastall + perl   Joseph Bedell
  • [Bioperl-l] RE: blastall + perl   Jason Stajich
• [Bioperl-l] Re: GO dbxrefs in swissprot   Hilmar Lapp
  • [Bioperl-l] Re: GO dbxrefs in swissprot   Andreas Henschel
    • [Bioperl-l] Re: GO dbxrefs in swissprot   Hilmar Lapp
      • [Bioperl-l] Re: GO dbxrefs in swissprot   Ewan Birney
      • [Bioperl-l] Re: GO dbxrefs in swissprot   Hilmar Lapp
• [Bioperl-l] Problems parsing swiss-prot files   Jessica Dantzer
  • [Bioperl-l] Problems parsing swiss-prot files   Jason Stajich
    • [Bioperl-l] Problems parsing swiss-prot files   Jessica Dantzer
• [Bioperl-l] Bio::Graphics - how to adjust height of a panel as you add more tracks?   Lincoln Stein
• [Bioperl-l] Bioperl: CVS and packages   Jonathan Manning
  • [Bioperl-l] Bioperl: CVS and packages   Brian Osborne
    • [Bioperl-l] Bioperl: CVS and packages   Jonathan Manning
• [Bioperl-l] Bioperl: CVS and packages   Davis, Sean (NIH/NHGRI)
  • [Bioperl-l] Bioperl: CVS and packages   James Thompson
    • [Bioperl-l] Bioperl: CVS and packages   Brian Osborne
• [Bioperl-l] PDB sequence from ATOM records   Alex Gutteridge
  • [Bioperl-l] PDB sequence from ATOM records   Jurgen Pletinckx
• [Bioperl-l] PDB sequence from ATOM records   Alex Gutteridge
  • [Bioperl-l] PDB sequence from ATOM records   Dave Howorth
    • [Bioperl-l] PDB sequence from ATOM records   Jurgen Pletinckx
• [Bioperl-l] Writing a Bio::Assembly::Contig using Bio::AlignIO   Lewis, Christopher
  • [Bioperl-l] Writing a Bio::Assembly::Contig using Bio::AlignIO   Aaron J Mackey
• [Bioperl-l] Writing a Bio::Assembly::Contig using Bio::AlignIO   Lewis, Christopher
• [Bioperl-l] Question about script bp_pairwise_kaks.pl   Jack Chen
  • [Bioperl-l] Question about script bp_pairwise_kaks.pl   Jason Stajich
• [Bioperl-l] Automating a fasta sequence submission   Stuart Gillies
  • [Bioperl-l] Automating a fasta sequence submission   Sean Davis
    • [Bioperl-l] Automating a fasta sequence submission   Boris Steipe
  • [Bioperl-l] Automating a fasta sequence submission   pdavid at netvisao.pt
  • [Bioperl-l] Automating a fasta sequence submission   Heikki Lehvaslaiho
• [Bioperl-l] How to fix "blast_report is undefined"??   Huizhuan Wu
• [Bioperl-l] piping to CAP3   James Gregory
• [Bioperl-l] Problem with genbank.pm ?   Alberto Davila
• [Bioperl-l] piping to CAP3   Marc Logghe
• [Bioperl-l] Help on a basic EST-genomic alignment script   Edward Chuong
• [Bioperl-l] PDB sequence from ATOM records   Matthew Betts
• [Bioperl-l] questions about the Bioperl installation.   Jane Sun
  • [Bioperl-l] questions about the Bioperl installation.   Barry Moore
• [Bioperl-l] Help with promoter analysis   gtg974p at mail.gatech.edu
• [Bioperl-l] Problem with Bio::TreeIO::nexus   Donald G. Jackson
• [Bioperl-l] Re: Problem with Bio::TreeIO::nexus   Jason Stajich
  • [Bioperl-l] Re: Problem with Bio::TreeIO::nexus   Donald G. Jackson
• [Bioperl-l] CSHL Computational Genomics - Application deadline July 15   William R.Pearson
• [Bioperl-l] wwwblast script question   huizhuan wu
  • [Bioperl-l] wwwblast script question   Jason Stajich
• [Bioperl-l] Sim4 help   Miroslava Cuperlovic-Culf
  • [Bioperl-l] Sim4 help   Brian Osborne
• [Bioperl-l] Few questions on whole chromosome & GFF   gtg974p at mail.gatech.edu
  • [Bioperl-l] Few questions on whole chromosome & GFF   Jason Stajich
• [Bioperl-l] subsequence with features, like biojava?   Wiepert, Mathieu
• [Bioperl-l] Questions from a Bioperl beginner?   jsun at biologicaltargets.com
  • [Bioperl-l] Questions from a Bioperl beginner?   Barry Moore
  • [Bioperl-l] Questions from a Bioperl beginner?   Jason Stajich
• [Bioperl-l] BIO::DB::Genbank problem handling Contigs with db->get_Stream_by_query($query);   ! Roievil !
  • [Bioperl-l] BIO::DB::Genbank problem handling Contigs with db->get_Stream_by_query($query);   Lincoln Stein
• [Bioperl-l] installation of bioperl-db   S.Paul
  • [Bioperl-l] installation of bioperl-db   Barry Moore
    • [Bioperl-l] installation of bioperl-db   S.Paul
  • [Bioperl-l] installation of bioperl-db   Jason Stajich
    • [Bioperl-l] installation of bioperl-db   Hilmar Lapp
• [Bioperl-l] Batch Entrez with Bio::DB:GenBank or Bio::DB:GenPept   Chris Fields
  • [Bioperl-l] Batch Entrez with Bio::DB:GenBank or Bio::DB:GenPept   Brian Osborne
  • [Bioperl-l] Batch Entrez with Bio::DB:GenBank or Bio::DB:GenPept   Lincoln Stein
    • [Bioperl-l] Batch Entrez with Bio::DB:GenBank or Bio::DB:GenPept   Chris Fields
• [Bioperl-l] pir.pm => bug   Laure.Durufle at serono.com
• [Bioperl-l] (no subject)   Laure.Durufle at serono.com
  • [Bioperl-l] multiple species in embl   Heikki Lehvaslaiho
• [Bioperl-l] Help on a basic EST-genomic alignment script   Edward Chuong
• [Bioperl-l] Added sequence parsing code to Bio::Tools::GFF   Chris Mungall
  • [Bioperl-l] Added sequence parsing code to Bio::Tools::GFF   Allen Day
    • [Bioperl-l] Added sequence parsing code to Bio::Tools::GFF   Chris Mungall
• [Bioperl-l] Re: [Bioperl-guts-l] bioperl commit   Aaron J. Mackey
  • [Bioperl-l] Re: [Bioperl-guts-l] bioperl commit   Chris Mungall
    • [Bioperl-l] Re: [Bioperl-guts-l] bioperl commit   Aaron J. Mackey
      • [Bioperl-l] Re: [Bioperl-guts-l] bioperl commit   Lincoln Stein
      • [Bioperl-l] Re: [Bioperl-guts-l] bioperl commit   Chris Mungall
• [Bioperl-l] new objects   Jason Stajich
• [Bioperl-l] remote blast and problem of connection on ncbi   gregory voisin
• [Bioperl-l] help us   j janani
• [Bioperl-l] Using a hash reference in the SeqFeature tag system   Leo, Paul (NIH/NHGRI)
  • [Bioperl-l] Using a hash reference in the SeqFeature tag system   Jason Stajich
  • [Bioperl-l] Using a hash reference in the SeqFeature tag system   Lincoln Stein
• [Bioperl-l] SeqFeatureCollection issue   Wiepert, Mathieu
  • [Bioperl-l] SeqFeatureCollection issue   Jason Stajich
• [Bioperl-l] Flat databases   S.Paul
  • [Bioperl-l] Flat databases   Lincoln Stein
  • [Bioperl-l] Flat databases   Lincoln Stein
  • [Bioperl-l] Flat databases   S.Paul
• [Bioperl-l] bp_bulk_load_gff.pl speed   Dustin Cram
  • [Bioperl-l] bp_bulk_load_gff.pl speed   Aaron J. Mackey
    • [Bioperl-l] bp_bulk_load_gff.pl speed   Dustin Cram
  • [Bioperl-l] bp_bulk_load_gff.pl speed   Aaron J. Mackey
• [Bioperl-l] Protein interaction modules   Richard Adams
  • [Bioperl-l] Protein interaction modules   Brian Osborne
• [Bioperl-l] SRS querying   Sean Davis
• [Bioperl-l] SeqFeatureCollection issue   Wiepert, Mathieu
  • [Bioperl-l] SeqFeatureCollection issue   Jason Stajich
• [Bioperl-l] tempdir() issues in regular perl.   Victor Weike Xin (Houston)
  • [Bioperl-l] tempdir() issues in regular perl.   Jason Stajich
• [Bioperl-l] Bio::Graphics Description layout question   Agrin, Nathan
• [Bioperl-l] SeqFeatureCollection issue   Wiepert, Mathieu
  • [Bioperl-l] SeqFeatureCollection issue   Jason Stajich
• [Bioperl-l] bp_bulk_load_gff.pl speed   Scott Cain
  • [Bioperl-l] bp_bulk_load_gff.pl speed   Aaron J. Mackey
  • [Bioperl-l] bp_bulk_load_gff.pl speed   Dustin Cram
    • [Bioperl-l] bp_bulk_load_gff.pl speed   Lincoln Stein
• [Bioperl-l] obtaining subsequences   Eric Wang
• [Bioperl-l] Bio::Graphics Description layout question   Roels, Steven
  • [Bioperl-l] Bio::Graphics Description layout question   Lincoln Stein
• [Bioperl-l] Re: [Bioperl-guts-l] bioperl commit   Aaron J Mackey
  • [Bioperl-l] Re: [Bioperl-guts-l] bioperl commit   Aaron J. Mackey
• [Bioperl-l] RE: strand in Meta-data sequence-region   Roels, Steven
• [Bioperl-l] display Newick trees   dimka
  • [Bioperl-l] display Newick trees   Jason Stajich
  • [Bioperl-l] display Newick trees   Arlin Stoltzfus
    • [Bioperl-l] display Newick trees   Jason Stajich
• [Bioperl-l] parallel processing with perl   gowthaman ramasamy
  • [Bioperl-l] parallel processing with perl   Peter Wilkinson
    • [Bioperl-l] parallel processing with perl   Jean-Jack Riethoven
      • [Bioperl-l] parallel processing with perl   Josh Lauricha
• [Bioperl-l] Bio::Graphics Description layout question   Agrin, Nathan
• [Bioperl-l] Bio::Graphics Description layout question   Roels, Steven
• [Bioperl-l] retreive medline records by title   Baranidharan P
• [Bioperl-l] Cookie problems   Tariq Shafi
  • [Bioperl-l] Cookie problems   Lincoln Stein
• [Bioperl-l] Cookie problems   Tariq Shafi
• [Bioperl-l] Blast Output and frac_aligned_query   James Wasmuth
  • [Bioperl-l] Blast Output and frac_aligned_query   Jason Stajich
    • [Bioperl-l] Blast Output and frac_aligned_query   Aaron J. Mackey
      • [Bioperl-l] Blast Output and frac_aligned_query   James Wasmuth
      • [Bioperl-l] Blast Output and frac_aligned_query   Aaron J. Mackey
• [Bioperl-l] Re: retreive medline records by title   Martin Senger
• [Bioperl-l] Validation of information loaded into bioperl-db   Law, Annie
  • [Bioperl-l] Validation of information loaded into bioperl-db   Hilmar Lapp
    • [Bioperl-l] Re: bioperl-db   Mike Muratet
      • [Bioperl-l] Re: bioperl-db   Hilmar Lapp
      • [Bioperl-l] Re: bioperl-db   Mike Muratet
      • [Bioperl-l] Re: bioperl-db   Hilmar Lapp
• [Bioperl-l] Bioperl support for AGAVE xml   Simon K. Chan
  • [Bioperl-l] Bioperl support for AGAVE xml   Brian Osborne
    • [Bioperl-l] Bioperl support for AGAVE xml   Simon K. Chan
      • [Bioperl-l] Bioperl support for AGAVE xml   Jason Stajich
      • [Bioperl-l] Bioperl support for AGAVE xml   Brian Osborne
      • [Bioperl-l] Bioperl support for AGAVE xml   Simon K. Chan
• [Bioperl-l] html stripped from blast report   ghrose at unm.edu
  • [Bioperl-l] html stripped from blast report   Brian Osborne
    • [Bioperl-l] html stripped from blast report   Jason Stajich
• [Bioperl-l] problem setting mismatch penalty in StandAloneBlast.pm without setting quiet()   Scott Markel
  • [Bioperl-l] problem setting mismatch penalty in StandAloneBlast.pm without setting quiet()   Jason Stajich
    • [Bioperl-l] problem setting mismatch penalty in StandAloneBlast.pm without setting quiet()   Scott Markel
• [Bioperl-l] Chou-Fasman   mark.schreiber at group.novartis.com
  • [Bioperl-l] Chou-Fasman   Aaron J. Mackey
• [Bioperl-l] All-vs-all BLAST   Peter J Stogios
  • [Bioperl-l] All-vs-all BLAST   Paulo Almeida
    • [Bioperl-l] All-vs-all BLAST   Jason Stajich
      • [Bioperl-l] All-vs-all BLAST   richard sucgang phd
      • [Bioperl-l] All-vs-all BLAST   Peter van Heusden
      • [Bioperl-l] All-vs-all BLAST   Andreas Kahari
      • [Bioperl-l] All-vs-all BLAST   Josh Lauricha
      • [Bioperl-l] All-vs-all BLAST   James Wasmuth
    • [Bioperl-l] All-vs-all BLAST   James Wasmuth
      • [Bioperl-l] All-vs-all BLAST   Jason Stajich
  • [Bioperl-l] All-vs-all BLAST   Tony Andreeva
    • [Bioperl-l] All-vs-all BLAST   James Wasmuth
• [Bioperl-l] Bio::Graphics::Panel   michael watson (IAH-C)
• [Bioperl-l] tmp-files   Sonja Funke
  • [Bioperl-l] tmp-files   Andreas Kahari
• [Bioperl-l] Bio::Graphics::Panel   Crabtree, Jonathan
• [Bioperl-l] Bio::Graphics funkiness   Josh Lauricha
  • [Bioperl-l] Bio::Graphics funkiness   Jean-Jack Riethoven
• [Bioperl-l] SwissProt/UniProt GN line format changed   Boris Lenhard
  • [Bioperl-l] SwissProt/UniProt GN line format changed   Hilmar Lapp
    • [Bioperl-l] SwissProt/UniProt GN line format changed   Ewan Birney
• [Bioperl-l] Load_ontology.pl warnings and exceptions   Law, Annie
  • [Bioperl-l] Load_ontology.pl warnings and exceptions   Hilmar Lapp
• [Bioperl-l] FW: Load_ontology.pl warnings and exceptions   Law, Annie
• [Bioperl-l] compiling ext-1.4 on solaris 2.9   Michal Kurowski
  • [Bioperl-l] compiling ext-1.4 on solaris 2.9   Aaron J. Mackey
    • [Bioperl-l] Re: compiling ext-1.4 on solaris 2.9   Michal Kurowski
• [Bioperl-l] compiling ext-1.4 on solaris 2.9   mkur at gazeta.pl
• [Bioperl-l] bioperl installation   Xiang Deng
• [Bioperl-l] bioperl installation   Brian Osborne
• [Bioperl-l] bioperl installation   Jason Stajich
  • [Bioperl-l] bioperl installation   Xiang Deng
• [Bioperl-l] Bioperl exceptions   Peter van Heusden
  • [Bioperl-l] Bioperl exceptions   Jason Stajich
• [Bioperl-l] Molecular weight calculation   Brian Osborne
• [Bioperl-l] bioperl installation   Brian Osborne
  • [Bioperl-l] bioperl installation   Xiang Deng
• [Bioperl-l] bioperl installation   Jason Stajich
  • [Bioperl-l] bioperl installation   Xiang Deng
• [Bioperl-l] StandAloneBlast.pm and RemoteBlast.pm   jwon at ucalgary.ca
  • [Bioperl-l] StandAloneBlast.pm and RemoteBlast.pm   Jason Stajich
• [Bioperl-l] bioperl installation   Jason Stajich
  • [Bioperl-l] bioperl installation   Xiang Deng
• [Bioperl-l] Trypic digest predictor   Agrin, Nathan
• [Fwd: Re: [Bioperl-l] installation!]   Barry Moore
• [Bioperl-l] Question about Fgenesh.pm   Andrew Nunberg
• FW: [Bioperl-l] Question about Fgenesh.pm   Andrew Nunberg
  • FW: [Bioperl-l] Question about Fgenesh.pm   Jason Stajich
• [Bioperl-l] Question about Fgenesh.pm   Jason Stajich
  • [Bioperl-l] Question about Fgenesh.pm   Chris Dwan
• [Bioperl-l] Retrieve results for an RID   Nurcan Mete
  • [Bioperl-l] Retrieve results for an RID   Jason Stajich
    • [Bioperl-l] Retrieve results for an RID   Nurcan Mete
      • [Bioperl-l] Retrieve results for an RID   Jason Stajich
      • [Bioperl-l] Retrieve results for an RID   Nurcan Mete
      • [Bioperl-l] Retrieve results for an RID   Jason Stajich
• [Bioperl-l] installation!   Malabika S
• [Bioperl-l] negative start/end numbers to Bio::SeqFeature::Generic   mql201
• [Bioperl-l] negative start/end numbers to Bio::SeqFeature::Generic   Crabtree, Jonathan
• [Bioperl-l] negative start/end numbers to Bio::SeqFeature::Generic   Crabtree, Jonathan
• [Bioperl-l] Help for using Clustalw.pm   Sun, Jian
  • [Bioperl-l] Help for using Clustalw.pm   James Wasmuth
    • [Bioperl-l] Help for using Clustalw.pm   James Wasmuth
• [Bioperl-l] Bio::SearchIO   davila
  • [Bioperl-l] Bio::SearchIO   Jason Stajich
• [Bioperl-l] Help for using Clustalw.pm   James Wasmuth
  • [Bioperl-l] Help for using Clustalw.pm   Jason Stajich
• [Bioperl-l] Getting chromosome from GenPept?   Leo, Paul (NIH/NHGRI)
  • [Bioperl-l] Getting chromosome from GenPept?   Barry Moore
• [Bioperl-l] ensembl database   Stuart Gillies
  • [Bioperl-l] ensembl database   Jonathan Manning
  • [Bioperl-l] ensembl database   Stefan Kirov
• [Bioperl-l] Help for using Clustalw.pm   Sun, Jian
• [Bioperl-l] Help for using Clustalw.pm   James Wasmuth
• [Bioperl-l] Help for using Clustalw.pm]   James Wasmuth
• [Bioperl-l] pdb files/structure system   Douglas Kojetin
  • [Bioperl-l] pdb files/structure system   Jurgen Pletinckx
    • [Bioperl-l] pdb files/structure system   Brian Osborne
      • [Bioperl-l] pdb files/structure system   Jurgen Pletinckx
• [Bioperl-l] Retrive the sequences from Blast report   Sun, Jian
  • [Bioperl-l] Retrive the sequences from Blast report   Sean Davis
    • [Bioperl-l] Retrive the sequences from Blast report   Jan Aerts
• [Bioperl-l] Bioperl Vista module and CGI   Jonathan Manning
• [Bioperl-l] Bioperl Vista module and CGI   Jonathan Manning
• [Bioperl-l] registry configuration and access   Michael Bradley
  • [Bioperl-l] registry configuration and access   Brian Osborne
• [Bioperl-l] error in Bio::Graphics print $panel->png   Miroslava Cuperlovic-Culf
  • [Bioperl-l] Re: error in Bio::Graphics print $panel->png   Jesper Krogh
  • [Bioperl-l] error in Bio::Graphics print $panel->png   Jason Stajich
• [Bioperl-l] Regarding Bio-Informatics Softwares.   amey vinod deshpande
  • [Bioperl-l] Regarding Bio-Informatics Softwares.   Brian Osborne
• [Bioperl-l] gibbs sampler question   Sean Davis
• [Bioperl-l] xml converter   rmaps005 at cib.csic.es
• [Bioperl-l] add in mail list   Zong-Li Xu
• [Bioperl-l] RNA fold   Michael Janis
  • [Bioperl-l] RNA fold   Chris Fields

Last message date: Sat Jul 31 14:05:41 EST 2004
Archived on: Sun Aug 1 18:10:43 EST 2004

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